Table of Contents
Project Information
report description
projects db info
taxonomy summary
genome size estimates
contamination summary
project base counts
Libraries and Reads
assembled average insert size estimates
library / read quality summary
reads2plates summary
trimmed read length histograms
library vector screening
GC Content of reads histogram
Contigs and Assemblies
contig size and read count table
depth summary
depth histogram
depth values
Assembler Specific Info
reads in assembly summary from assembler
assembly parameters
Project Information
-------------------------------------------------------------------
Assembly QC Report
Date: 12-12-2005
Runby: Kerrie Barry
Description: analysis of libraries in progress (or initial analysis of completed)
-------------------------------------------------------------------
-------------------------------------------------------------------
Project information from 'PROJECTS' db
-------------------------------------------------------------------
Project Size(KB) TaxID GenusSpecies
3634608 4500 NULL Shewanella putrefaciens
-------------------------------------------------------------------
Taxonomy summary
Command: /home/copeland/scripts/tax2tree.sh Shewanella_putrefaciens
-------------------------------------------------------------------
Shewanellaceae, family, g-proteobacteria
Alteromonadales, order, g-proteobacteria
Shewanella putrefaciens, species, g-proteobacteria
Shewanella, genus, g-proteobacteria
Gammaproteobacteria, class, g-proteobacteria
Proteobacteria (purple bacteria), phylum, proteobacteria
Bacteria (eubacteria), superkingdom, eubacteria
cellular organisms
root
-------------------------------------------------------------------
Genome size estimates
-------------------------------------------------------------------
# contigs: 5238479
# phrap: 3311770
# db:
altered.
4500000
4350083 +/- 793686
-------------------------------------------------------------------
Contam Summary with *.contigs:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o
-------------------------------------------------------------------
Number of reads with X's: 3984
Number of reads with percent X's >= 20%: 648 = 4.2%
Number of reads with percent X's >= 50%: 598 = 3.9%
Number of reads with percent X's >= 80%: 492 = 3.2%
Total reads in project: 15264
Total bp X'd : 668249
reads >= 20% >= 50% >= 80% screened
Nr with L09136 3416 95 66 44
Nr with LRS 36 36 36 29
Nr with pMCL200_JGI_XZX+XZK 532 517 496 419
-------------------------------------------------------------------
Contam Summary with *.singlets:
Command: /psf/QC/bin/sparc/summarizeCrossMatchHits -o -s
-------------------------------------------------------------------
Number of reads with X's: 807
Number of reads with percent X's >= 20%: 524 = 24.2%
Number of reads with percent X's >= 50%: 514 = 23.7%
Number of reads with percent X's >= 80%: 459 = 21.2%
Total reads in project: 2167
Total bp X'd : 481230
reads >= 20% >= 50% >= 80% screened
Nr with L09136 322 44 43 42
Nr with LRS 36 36 36 29
Nr with pMCL200_JGI_XZX+XZK 449 444 435 388
-------------------------------------------------------------------
Base Count for Project:
Command: /home/copeland/scripts/projectBaseCount.pl phrap.out
-------------------------------------------------------------------
A = 3641507
C = 3632955
G = 3540901
T = 3657878
N = 50798
X = 668249
GC fraction = 0.47
Total = 15192288
-------------------------------------------------------------------
Base Count for contigs:
Command: /psf/QC/bin/sparc/faCount 3634608_fasta.screen.contigs
-------------------------------------------------------------------
A 1424922
C 1385113
G 1378040
T 1420985
N 78817
fraction GC = 0.49
total bases = 5687877
Libraries and Reads
-------------------------------------------------------------------
Histogram of Assembled Average Insert Sizes:
Command: /home/copeland/scripts/phrapView2.pl -p phrap.out -C > reads.list
-------------------------------------------------------------------
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIOS reads.list > grep.reads.list.AIOS
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIOS 4 500
-------------------------------------------------------------------
#Found 805 total values totalling 2604717.0000. <3235.673292 +/- 650.731965>
#Range: [ 1011 - 5227 ]
#Most likely bin: [ 3000 - 3500 ] 267 counts
#Median bin: [ 3000 - 3500 ] 267 counts
#Histogram Bins Count Fraction Cum_Fraction
|X 1000 - 1500 : [ 7 0.01 0.01 ]
|XXXX 1500 - 2000 : [ 30 0.04 0.05 ]
|XXXXXX 2000 - 2500 : [ 37 0.05 0.09 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2500 - 3000 : [ 216 0.27 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 3000 - 3500 : [ 267 0.33 0.69 ]
|XXXXXXXXXXXXXXXXXXXXXX 3500 - 4000 : [ 148 0.18 0.88 ]
|XXXXXXXXXXXX 4000 - 4500 : [ 78 0.10 0.97 ]
|XXX 4500 - 5000 : [ 19 0.02 1.00 ]
| 5000 - 5500 : [ 3 0.00 1.00 ]
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIOT reads.list > grep.reads.list.AIOT
Command: /home/copeland/scripts/histogram2.pl grep.reads.list.AIOT 4 500
-------------------------------------------------------------------
#Found 126 total values totalling 762852.0000. <6054.380952 +/- 1750.700857>
#Range: [ 1146 - 8824 ]
#Most likely bin: [ 6500 - 7000 ] 32 counts
#Median bin: [ 6000 - 6500 ] 26 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXX 1000 - 1500 : [ 4 0.03 0.03 ]
|XXXX 1500 - 2000 : [ 3 0.02 0.06 ]
|XXXXX 2000 - 2500 : [ 4 0.03 0.09 ]
|XX 2500 - 3000 : [ 2 0.02 0.10 ]
|XX 3000 - 3500 : [ 2 0.02 0.12 ]
|XXXX 3500 - 4000 : [ 3 0.02 0.14 ]
|XXXXXX 4000 - 4500 : [ 5 0.04 0.18 ]
#...
|XX 5000 - 5500 : [ 2 0.02 0.20 ]
|XXXXXXXXXXXXXXX 5500 - 6000 : [ 12 0.10 0.29 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6000 - 6500 : [ 26 0.21 0.50 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 6500 - 7000 : [ 32 0.25 0.75 ]
|XXXXXXXXXXXXXXXXXXX 7000 - 7500 : [ 15 0.12 0.87 ]
|XXXXXXXXX 7500 - 8000 : [ 7 0.06 0.93 ]
|XXXX 8000 - 8500 : [ 3 0.02 0.95 ]
|XXXXXXXX 8500 - 9000 : [ 6 0.05 1.00 ]
-------------------------------------------------------------------
Estimated Assembled Average Insert Sizes:
Command: /home/copeland/scripts/estInsertSize.pl -f phrap.out
-------------------------------------------------------------------
# AIOS 3222 +- 681 (n=809)
# AIOT 6054 +- 1758 (n=126)
-------------------------------------------------------------------
Library / Read Quality summary
extracted from 3634608_fasta.screen.trimQ15.SaF and database (md_run table)
* note J15 is Jazz trimmed length, Q20 is count of Quality 20+ bases
-------------------------------------------------------------------
DB |----J15---| |----Q20---| Fasta |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AIOS 7680 -1 -1 96 748 7680 95 772 97 775
AIOT 7680 -1 -1 96 696 7584 89 734 96 725
FWD |----J15---| |----Q20---| REV |----J15---| |----Q20---|
LIB Reads %pass AvgLen %pass AvgNum Reads %pass AvgLen %pass AvgNun
AIOS 3840 97 755 98 770 3840 93 789 95 781
AIOT 3744 89 732 97 722 3840 90 736 96 727
-------------------------------------------------------------------
reads2plates summary
extracted from file: 3634608_fasta.screen.r2p [ from "READ/CLONE COUNT SUMMARY" to end ]
-------------------------------------------------------------------
plate(s) reads clones N/plate avg% LIBRARY @
40 7680 3840 96.00 100.00 AIOS @
40 7584 3840 96.00 100.00 AIOT @
] 15264 7680 96.00 cumulative total@@
LIBRARY PLATE ID COUNT [ AIOS 40 AIOT 40 ] for 80 total 96 well plate ids.
Only indicates plates present in input file.
Make no assumption regarding plates (not) present in project that do not appear above.
-------------------------------------------------------------------
trimt JAZZ trim 15 readlength histogram:
Command: /home/copeland/scripts/histogram2.pl 3634608_fasta.screen.trimQ15.SaF 4 50
-------------------------------------------------------------------
#Found 15264 total values totalling 10616011.0000. <695.493383 +/- 226.144882>
#Range: [ 0 - 946 ]
#Most likely bin: [ 750 - 800 ] 4815 counts
#Median bin: [ 750 - 800 ] 4815 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXX 0 - 50 : [ 1128 0.07 0.07 ]
|X 50 - 100 : [ 64 0.00 0.08 ]
| 100 - 150 : [ 31 0.00 0.08 ]
| 150 - 200 : [ 31 0.00 0.08 ]
| 200 - 250 : [ 47 0.00 0.09 ]
| 250 - 300 : [ 52 0.00 0.09 ]
|X 300 - 350 : [ 94 0.01 0.09 ]
|X 350 - 400 : [ 122 0.01 0.10 ]
|X 400 - 450 : [ 162 0.01 0.11 ]
|X 450 - 500 : [ 143 0.01 0.12 ]
|XX 500 - 550 : [ 184 0.01 0.13 ]
|XX 550 - 600 : [ 191 0.01 0.15 ]
|XX 600 - 650 : [ 271 0.02 0.17 ]
|XXXXX 650 - 700 : [ 646 0.04 0.21 ]
|XXXXXXXXXXXXXXXXXXX 700 - 750 : [ 2303 0.15 0.36 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 4815 0.32 0.67 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 4080 0.27 0.94 ]
|XXXXXXX 850 - 900 : [ 879 0.06 1.00 ]
| 900 - 950 : [ 21 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIOS
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIOS 3634608_fasta.screen.trimQ15.SaF > reads.trim15.AIOS.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIOS.rl 2 50
-------------------------------------------------------------------
#Found 7680 total values totalling 5639016.0000. <734.246875 +/- 183.558355>
#Range: [ 0 - 946 ]
#Most likely bin: [ 750 - 800 ] 2767 counts
#Median bin: [ 750 - 800 ] 2767 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXX 0 - 50 : [ 360 0.05 0.05 ]
| 50 - 100 : [ 16 0.00 0.05 ]
| 100 - 150 : [ 9 0.00 0.05 ]
| 150 - 200 : [ 7 0.00 0.05 ]
| 200 - 250 : [ 18 0.00 0.05 ]
| 250 - 300 : [ 19 0.00 0.06 ]
| 300 - 350 : [ 17 0.00 0.06 ]
| 350 - 400 : [ 19 0.00 0.06 ]
| 400 - 450 : [ 21 0.00 0.06 ]
| 450 - 500 : [ 33 0.00 0.07 ]
|X 500 - 550 : [ 46 0.01 0.07 ]
|X 550 - 600 : [ 43 0.01 0.08 ]
|X 600 - 650 : [ 83 0.01 0.09 ]
|XXXX 650 - 700 : [ 267 0.03 0.12 ]
|XXXXXXXXXXXXXXXXXX 700 - 750 : [ 1228 0.16 0.28 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 2767 0.36 0.64 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 2218 0.29 0.93 ]
|XXXXXXX 850 - 900 : [ 495 0.06 1.00 ]
| 900 - 950 : [ 14 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIOT
-------------------------------------------------------------------
Command: /usr/xpg4/bin/grep AIOT 3634608_fasta.screen.trimQ15.SaF > reads.trim15.AIOT.rl
Command: /home/copeland/scripts/histogram2.pl reads.trim15.AIOT.rl 2 50
-------------------------------------------------------------------
#Found 7584 total values totalling 4976995.0000. <656.249341 +/- 256.416196>
#Range: [ 0 - 918 ]
#Most likely bin: [ 750 - 800 ] 2048 counts
#Median bin: [ 750 - 800 ] 2048 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXX 0 - 50 : [ 768 0.10 0.10 ]
|X 50 - 100 : [ 48 0.01 0.11 ]
| 100 - 150 : [ 22 0.00 0.11 ]
| 150 - 200 : [ 24 0.00 0.11 ]
|X 200 - 250 : [ 29 0.00 0.12 ]
|X 250 - 300 : [ 33 0.00 0.12 ]
|XX 300 - 350 : [ 77 0.01 0.13 ]
|XX 350 - 400 : [ 103 0.01 0.15 ]
|XXX 400 - 450 : [ 141 0.02 0.16 ]
|XX 450 - 500 : [ 110 0.01 0.18 ]
|XXX 500 - 550 : [ 138 0.02 0.20 ]
|XXX 550 - 600 : [ 148 0.02 0.22 ]
|XXXX 600 - 650 : [ 188 0.02 0.24 ]
|XXXXXXX 650 - 700 : [ 379 0.05 0.29 ]
|XXXXXXXXXXXXXXXXXXXXX 700 - 750 : [ 1075 0.14 0.43 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 750 - 800 : [ 2048 0.27 0.70 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 800 - 850 : [ 1862 0.25 0.95 ]
|XXXXXXXX 850 - 900 : [ 384 0.05 1.00 ]
| 900 - 950 : [ 7 0.00 1.00 ]
trimt JAZZ trim 15 readlength histogram for AIOU
-------------------------------------------------------------------
Library vector screening
Command: /home/copeland/scripts/checkScreen.sh 3634608
-------------------------------------------------------------------
AIOS.000001.000100 pUC18.fa LRS.fasta
AIOT.000001.000100 pMCL200.fa LRS.fasta
AIOS.000001.000100 pUC18.fa LRS.fasta
AIOT.000001.000100 pMCL200.fa LRS.fasta
-------------------------------------------------------------------
GC content histogram:
Command: /bin/nawk '{print $5+$6}' GC.3634608_fasta.screen.trimQ20 | /home/copeland/scripts/histogram2.pl - 1 0.005
-------------------------------------------------------------------
# GC.3634608_fasta.screen.trimQ20 | nawk 'NR>1 {print $5+$6}' | /home/jchapman/perlscripts/histogram2.pl - 1 0.005
#Found 14157 total values totalling 6969.4307. <0.492296 +/- 0.063287>
#Range: [ 0.24 - 0.7627 ]
#Most likely bin: [ 0.54 - 0.545 ] 424 counts
#Median bin: [ 0.49 - 0.495 ] 286 counts
#Entropy = 5.6309 bits
| 0.24 - 0.245 : [ 1 7.06e-05 7.06e-05 1 ]
#...
| 0.275 - 0.28 : [ 4 2.83e-04 3.53e-04 5 ]
|X 0.28 - 0.285 : [ 6 4.24e-04 7.77e-04 11 ]
| 0.285 - 0.29 : [ 5 3.53e-04 1.13e-03 16 ]
| 0.29 - 0.295 : [ 3 2.12e-04 1.34e-03 19 ]
|X 0.295 - 0.3 : [ 9 6.36e-04 1.98e-03 28 ]
|X 0.3 - 0.305 : [ 12 8.48e-04 2.83e-03 40 ]
|X 0.305 - 0.31 : [ 7 4.94e-04 3.32e-03 47 ]
| 0.31 - 0.315 : [ 5 3.53e-04 3.67e-03 52 ]
|X 0.315 - 0.32 : [ 7 4.94e-04 4.17e-03 59 ]
|X 0.32 - 0.325 : [ 15 1.06e-03 5.23e-03 74 ]
|X 0.325 - 0.33 : [ 9 6.36e-04 5.86e-03 83 ]
|XX 0.33 - 0.335 : [ 24 1.70e-03 7.56e-03 107 ]
|XX 0.335 - 0.34 : [ 19 1.34e-03 8.90e-03 126 ]
|XX 0.34 - 0.345 : [ 19 1.34e-03 1.02e-02 145 ]
|XXX 0.345 - 0.35 : [ 27 1.91e-03 1.21e-02 172 ]
|XXX 0.35 - 0.355 : [ 32 2.26e-03 1.44e-02 204 ]
|XXXX 0.355 - 0.36 : [ 42 2.97e-03 1.74e-02 246 ]
|XXXXX 0.36 - 0.365 : [ 49 3.46e-03 2.08e-02 295 ]
|XXXXXX 0.365 - 0.37 : [ 59 4.17e-03 2.50e-02 354 ]
|XXXXXX 0.37 - 0.375 : [ 66 4.66e-03 2.97e-02 420 ]
|XXXXXXX 0.375 - 0.38 : [ 78 5.51e-03 3.52e-02 498 ]
|XXXXXXXX 0.38 - 0.385 : [ 82 5.79e-03 4.10e-02 580 ]
|XXXXXXXXX 0.385 - 0.39 : [ 92 6.50e-03 4.75e-02 672 ]
|XXXXXXXXXXX 0.39 - 0.395 : [ 114 8.05e-03 5.55e-02 786 ]
|XXXXXXXXXXXXXXXXX 0.395 - 0.4 : [ 183 1.29e-02 6.84e-02 969 ]
|XXXXXXXXXXXXXXXX 0.4 - 0.405 : [ 166 1.17e-02 8.02e-02 1135 ]
|XXXXXXXXXXXXXXXXXXXXX 0.405 - 0.41 : [ 223 1.58e-02 9.59e-02 1358 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.41 - 0.415 : [ 264 1.86e-02 1.15e-01 1622 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 0.415 - 0.42 : [ 262 1.85e-02 1.33e-01 1884 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.42 - 0.425 : [ 332 2.35e-02 1.57e-01 2216 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.425 - 0.43 : [ 328 2.32e-02 1.80e-01 2544 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.43 - 0.435 : [ 343 2.42e-02 2.04e-01 2887 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.435 - 0.44 : [ 364 2.57e-02 2.30e-01 3251 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.44 - 0.445 : [ 380 2.68e-02 2.56e-01 3631 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.445 - 0.45 : [ 411 2.90e-02 2.86e-01 4042 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.45 - 0.455 : [ 398 2.81e-02 3.14e-01 4440 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.455 - 0.46 : [ 389 2.75e-02 3.41e-01 4829 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.46 - 0.465 : [ 378 2.67e-02 3.68e-01 5207 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.465 - 0.47 : [ 353 2.49e-02 3.93e-01 5560 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.47 - 0.475 : [ 334 2.36e-02 4.16e-01 5894 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.475 - 0.48 : [ 320 2.26e-02 4.39e-01 6214 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.48 - 0.485 : [ 303 2.14e-02 4.60e-01 6517 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.485 - 0.49 : [ 342 2.42e-02 4.84e-01 6859 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXX 0.49 - 0.495 : [ 286 2.02e-02 5.05e-01 7145 ]
|XXXXXXXXXXXXXXXXXXXXXXXX 0.495 - 0.5 : [ 254 1.79e-02 5.23e-01 7399 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.5 - 0.505 : [ 320 2.26e-02 5.45e-01 7719 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.505 - 0.51 : [ 306 2.16e-02 5.67e-01 8025 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.51 - 0.515 : [ 295 2.08e-02 5.88e-01 8320 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.515 - 0.52 : [ 337 2.38e-02 6.11e-01 8657 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.52 - 0.525 : [ 365 2.58e-02 6.37e-01 9022 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.525 - 0.53 : [ 386 2.73e-02 6.65e-01 9408 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.53 - 0.535 : [ 409 2.89e-02 6.93e-01 9817 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.535 - 0.54 : [ 388 2.74e-02 7.21e-01 10205 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.54 - 0.545 : [ 424 2.99e-02 7.51e-01 10629 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.545 - 0.55 : [ 405 2.86e-02 7.79e-01 11034 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.55 - 0.555 : [ 421 2.97e-02 8.09e-01 11455 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.555 - 0.56 : [ 418 2.95e-02 8.39e-01 11873 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.56 - 0.565 : [ 368 2.60e-02 8.65e-01 12241 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.565 - 0.57 : [ 364 2.57e-02 8.90e-01 12605 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXX 0.57 - 0.575 : [ 298 2.10e-02 9.11e-01 12903 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXX 0.575 - 0.58 : [ 280 1.98e-02 9.31e-01 13183 ]
|XXXXXXXXXXXXXXXXXXXXXXX 0.58 - 0.585 : [ 241 1.70e-02 9.48e-01 13424 ]
|XXXXXXXXXXXXXXXXXXXX 0.585 - 0.59 : [ 212 1.50e-02 9.63e-01 13636 ]
|XXXXXXXXXXXXXXXX 0.59 - 0.595 : [ 166 1.17e-02 9.75e-01 13802 ]
|XXXXXXXXX 0.595 - 0.6 : [ 98 6.92e-03 9.82e-01 13900 ]
|XXXXXXX 0.6 - 0.605 : [ 76 5.37e-03 9.87e-01 13976 ]
|XXXXXX 0.605 - 0.61 : [ 62 4.38e-03 9.92e-01 14038 ]
|XXX 0.61 - 0.615 : [ 33 2.33e-03 9.94e-01 14071 ]
|XX 0.615 - 0.62 : [ 25 1.77e-03 9.96e-01 14096 ]
|XX 0.62 - 0.625 : [ 16 1.13e-03 9.97e-01 14112 ]
|X 0.625 - 0.63 : [ 11 7.77e-04 9.98e-01 14123 ]
|X 0.63 - 0.635 : [ 12 8.48e-04 9.98e-01 14135 ]
| 0.635 - 0.64 : [ 4 2.83e-04 9.99e-01 14139 ]
| 0.64 - 0.645 : [ 5 3.53e-04 9.99e-01 14144 ]
| 0.645 - 0.65 : [ 2 1.41e-04 9.99e-01 14146 ]
| 0.65 - 0.655 : [ 1 7.06e-05 9.99e-01 14147 ]
#...
| 0.66 - 0.665 : [ 1 7.06e-05 9.99e-01 14148 ]
| 0.665 - 0.67 : [ 2 1.41e-04 1.00e+00 14150 ]
#...
| 0.68 - 0.685 : [ 1 7.06e-05 1.00e+00 14151 ]
| 0.685 - 0.69 : [ 1 7.06e-05 1.00e+00 14152 ]
#...
| 0.715 - 0.72 : [ 1 7.06e-05 1.00e+00 14153 ]
| 0.72 - 0.725 : [ 1 7.06e-05 1.00e+00 14154 ]
#...
| 0.73 - 0.735 : [ 1 7.06e-05 1.00e+00 14155 ]
#...
| 0.745 - 0.75 : [ 1 7.06e-05 1.00e+00 14156 ]
#...
| 0.76 - 0.765 : [ 1 7.06e-05 1.00e+00 14157 ]
Contigs and Assemblies
-------------------------------------------------------------------
Command: /usr/local/bin/contig > contig.out [ final 30 lines ]
-------------------------------------------------------------------
Contig 2614. 24 reads; 7005 bp (untrimmed), 6580 (trimmed).
Contig 2615. 25 reads; 6759 bp (untrimmed), 6501 (trimmed).
Contig 2616. 25 reads; 7866 bp (untrimmed), 7737 (trimmed).
Contig 2617. 25 reads; 9525 bp (untrimmed), 9458 (trimmed).
Contig 2618. 25 reads; 10163 bp (untrimmed), 9924 (trimmed).
Contig 2619. 25 reads; 6709 bp (untrimmed), 6415 (trimmed).
Contig 2620. 26 reads; 7526 bp (untrimmed), 7483 (trimmed).
Contig 2621. 26 reads; 5165 bp (untrimmed), 5124 (trimmed).
Contig 2622. 26 reads; 10842 bp (untrimmed), 10764 (trimmed).
Contig 2623. 26 reads; 10697 bp (untrimmed), 10579 (trimmed).
Contig 2624. 27 reads; 8084 bp (untrimmed), 8025 (trimmed).
Contig 2625. 29 reads; 11097 bp (untrimmed), 10591 (trimmed).
Contig 2626. 29 reads; 9760 bp (untrimmed), 9694 (trimmed).
Contig 2627. 30 reads; 7631 bp (untrimmed), 7487 (trimmed).
Contig 2628. 30 reads; 10508 bp (untrimmed), 10317 (trimmed).
Contig 2629. 31 reads; 9146 bp (untrimmed), 9074 (trimmed).
Contig 2630. 37 reads; 9353 bp (untrimmed), 9238 (trimmed).
Contig 2631. 37 reads; 10332 bp (untrimmed), 10163 (trimmed).
Contig 2632. 41 reads; 8673 bp (untrimmed), 8458 (trimmed).
Contig 2633. 42 reads; 12191 bp (untrimmed), 12147 (trimmed).
Contig 2634. 47 reads; 9061 bp (untrimmed), 9015 (trimmed).
Contig 2635. 47 reads; 9041 bp (untrimmed), 8996 (trimmed).
Contig 2636. 49 reads; 13952 bp (untrimmed), 13899 (trimmed).
Contig 2637. 59 reads; 11725 bp (untrimmed), 11594 (trimmed).
Contig 2638. 106 reads; 21888 bp (untrimmed), 21815 (trimmed).
Contig 2639. 125 reads; 19019 bp (untrimmed), 18976 (trimmed).
Contig 2640. 127 reads; 23132 bp (untrimmed), 23063 (trimmed).
--------------------------------------------------------------
Totals 13097 reads; 5687877 bp (untrimmed), 5238479 (trimmed).
-------------------------------------------------------------------
Depth Summary
Command: /home/copeland/scripts/depth_summary.pl depth.out
-------------------------------------------------------------------
depth.out contains 5499360 bases = 2.19 +- 1.29 = 0.68 +- 1.40
-------------------------------------------------------------------
Histogram of All Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5
-------------------------------------------------------------------
#Found 2445 total values totalling 4922.3000. <2.013211 +/- 0.620682>
#Range: [ 1.04 - 6.20 ]
#Most likely bin: [ 1.5 - 2 ] 919 counts
#Median bin: [ 1.5 - 2 ] 919 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXXXXXXXXXXXXXXXXXXX 1 - 1.5 : [ 486 0.20 0.20 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 1.5 - 2 : [ 919 0.38 0.57 ]
|XXXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 570 0.23 0.81 ]
|XXXXXXXXXXXXX 2.5 - 3 : [ 299 0.12 0.93 ]
|XXXXX 3 - 3.5 : [ 114 0.05 0.98 ]
|XX 3.5 - 4 : [ 39 0.02 0.99 ]
| 4 - 4.5 : [ 8 0.00 1.00 ]
| 4.5 - 5 : [ 5 0.00 1.00 ]
| 5 - 5.5 : [ 3 0.00 1.00 ]
| 5.5 - 6 : [ 1 0.00 1.00 ]
| 6 - 6.5 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Histogram of Major Contig Depth Values:
Command: /home/copeland/scripts/histogram2.pl depth.out 9 0.5 3 10 10000000 5 2000 10000000
-------------------------------------------------------------------
#Found 273 total values totalling 771.8300. <2.827216 +/- 0.647321>
#Range: [ 1.67 - 6.20 ]
#Most likely bin: [ 2.5 - 3 ] 101 counts
#Median bin: [ 2.5 - 3 ] 101 counts
#Histogram Bins Count Fraction Cum_Fraction
|XXXX 1.5 - 2 : [ 11 0.04 0.04 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2 - 2.5 : [ 80 0.29 0.33 ]
|XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 2.5 - 3 : [ 101 0.37 0.70 ]
|XXXXXXXXXXXXXXXXXXXXX 3 - 3.5 : [ 52 0.19 0.89 ]
|XXXXXX 3.5 - 4 : [ 15 0.05 0.95 ]
|XX 4 - 4.5 : [ 6 0.02 0.97 ]
|XX 4.5 - 5 : [ 4 0.01 0.99 ]
|X 5 - 5.5 : [ 3 0.01 1.00 ]
#...
| 6 - 6.5 : [ 1 0.00 1.00 ]
-------------------------------------------------------------------
Sorted Depth Values:
Command: sort -n -k 9 depth.out > sorted.depth.out [first and last 20 lines included]
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Contig 265 2 reads 1806 bases = 1.04 +- 0.19 = -0.01 +- 0.98
Contig 419 2 reads 1627 bases = 1.04 +- 0.21 = 0.06 +- 0.98
Contig 766 2 reads 1825 bases = 1.04 +- 0.19 = 1.04 +- 0.19
Contig 773 2 reads 1888 bases = 1.04 +- 0.19 = -0.04 +- 0.98
Contig 203 2 reads 1855 bases = 1.05 +- 0.23 = 1.05 +- 0.23
Contig 334 2 reads 1594 bases = 1.05 +- 0.21 = 0.23 +- 0.95
Contig 426 2 reads 1806 bases = 1.05 +- 0.22 = 0.04 +- 0.97
Contig 631 2 reads 1855 bases = 1.05 +- 0.21 = -0.05 +- 0.97
Contig 640 2 reads 1848 bases = 1.05 +- 0.23 = -0.01 +- 0.97
Contig 789 2 reads 1826 bases = 1.05 +- 0.21 = 1.05 +- 0.21
Contig 260 2 reads 1848 bases = 1.06 +- 0.23 = -0.03 +- 0.97
Contig 300 2 reads 1805 bases = 1.06 +- 0.24 = -0.02 +- 0.97
Contig 319 2 reads 1866 bases = 1.06 +- 0.24 = 1.06 +- 0.24
Contig 400 2 reads 1776 bases = 1.06 +- 0.23 = 1.06 +- 0.23
Contig 487 2 reads 1867 bases = 1.06 +- 0.25 = -0.02 +- 0.97
Contig 659 2 reads 1870 bases = 1.06 +- 0.24 = 0.01 +- 0.97
Contig 204 2 reads 1728 bases = 1.07 +- 0.26 = 0.07 +- 0.96
Contig 250 2 reads 1772 bases = 1.07 +- 0.25 = 1.07 +- 0.25
Contig 609 2 reads 1857 bases = 1.07 +- 0.25 = 1.07 +- 0.25
Contig 670 2 reads 1793 bases = 1.07 +- 0.25 = 1.07 +- 0.25
Contig 2255 8 reads 1929 bases = 3.88 +- 1.33 = 0.08 +- 0.79
Contig 2055 6 reads 1446 bases = 3.91 +- 1.70 = 1.28 +- 0.87
Contig 2586 19 reads 4417 bases = 4.03 +- 1.74 = -0.26 +- 1.12
Contig 2356 9 reads 2113 bases = 4.10 +- 1.31 = 2.38 +- 0.84
Contig 2196 7 reads 1550 bases = 4.16 +- 1.92 = 1.71 +- 1.02
Contig 2371 10 reads 2048 bases = 4.16 +- 1.67 = 1.60 +- 1.53
Contig 2632 41 reads 8673 bases = 4.33 +- 2.12 = -0.21 +- 2.44
Contig 2408 10 reads 2141 bases = 4.40 +- 2.13 = 2.61 +- 2.49
Contig 2488 13 reads 2758 bases = 4.40 +- 1.35 = 3.04 +- 1.30
Contig 2638 106 reads 21888 bases = 4.44 +- 2.19 = -0.23 +- 2.23
Contig 2621 26 reads 5165 bases = 4.70 +- 3.07 = 2.10 +- 1.83
Contig 2637 59 reads 11725 bases = 4.71 +- 1.67 = -0.16 +- 2.50
Contig 2059 6 reads 1195 bases = 4.75 +- 1.74 = -0.20 +- 1.03
Contig 2635 47 reads 9041 bases = 4.82 +- 2.55 = 0.12 +- 2.27
Contig 2634 47 reads 9061 bases = 4.84 +- 1.79 = 1.67 +- 2.29
Contig 2640 127 reads 23132 bases = 5.04 +- 4.06 = 0.13 +- 2.36
Contig 2582 19 reads 3347 bases = 5.29 +- 4.76 = 2.03 +- 2.49
Contig 2499 13 reads 2070 bases = 5.32 +- 3.55 = 1.03 +- 1.63
Contig 2251 8 reads 1287 bases = 5.78 +- 2.27 = 2.77 +- 2.15
Contig 2639 125 reads 19019 bases = 6.20 +- 2.43 = 0.25 +- 2.45
Assembler Specific Info
-------------------------------------------------------------------
Reads in assembly summary
-------------------------------------------------------------------
Small Inserts = 284
HQ Discrepant reads = 324
Chimeric reads = 95
Suspect alignments = 40
-------------------------------------------------------------------
Assembly parameters
-------------------------------------------------------------------
phrap version SPS - 4.18 SUN Solaris 7,8
Score matrix /psf/QC/Applications/pphrap/matrix/score_matrix
A C G T N X
A 1 -2 -2 -2 0 0
C -2 1 -2 -2 0 0
G -2 -2 1 -2 0 0
T -2 -2 -2 1 0 0
N 0 0 0 0 0 0
X 0 0 0 0 0 0
gap_init: -4
gap_ext: -3
ins_gap_ext: -3
del_gap_ext: -3
Using complexity-adjusted scores. Assumed background frequencies:
A: 0.250 C: 0.250 G: 0.250 T: 0.250 N: 0.000 X: 0.000
minmatch: 30
maxmatch: 55
max_group_size: 20
minscore: 55
bandwidth: 14
indexwordsize: 10
vector_bound: 20
word_raw: 0
trim_penalty: -2
trim_score: 20
trim_qual: 13
maxgap: 30
repeat_stringency: 0.950000
qual_show: 20
confirm_length: 8
confirm_trim: 1
confirm_penalty: -5
confirm_score: 30
node_seg: 8
node_space: 4
forcelevel: 0
bypasslevel: 1
File generated in /psf/project/microbe3/3634608/edit_dir.26Oct05.QC